Bioinformatics

Bioinformatics Office Hours

The core facility is hosting Office Hours each second and fourth Thursday of the month (excluding holidays) at MOLR 145 (Morrison building/Virology) on East Campus from 1pm to 5pm. All are welcome with questions about bioinformatics (e.g. what software to use for your analyses), experimental design (e.g. which sequencing platform and depth to use), data management, etc. The dates are : Sep 27, Oct 11, Oct 25, Nov 8, and Dec 13. Follow @unl_bcrf for the latest news.

NU Core Facility - New User Program extended for FY18/19

The Nebraska Research Initiative, together with the Office of Research and Economic Development, has established a Core Facility Grant Program for New Users. Details may be found in this F18/19 document or at the grant's web page http://research.unl.edu/core-facility-grant-program-for-new-users/. If you are a new user and looking for Bioinformatics help, make use of this great opportunity at no cost to you.

Services

The UNL Bioinformatics Core Research Facility (BCRF) is located in the Beadle Center at the east side of the City Campus. The Core offers education, analysis, and computational services in the area of bioinformatics and computational biology.

We provide various standard bioinformatics services (listed under Service Fees) with a quick turnaround time and very reasonable fees.

Besides the listed services for fees, we also:

Help with preparing for and writing of grant proposals that include life sciences related computation or analyses. Free if the BCRF is included in the grant.

Collaborate on larger projects and grants (please talk to us first to request a quote)

Custom-program solutions (Java, Perl, VBA) for something simple as conversion or integration of data files, or on the other end of the spectrum develop and program solutions for large-scale analyses (billed per hour)

Give lectures in bioinformatics topics

Install and maintain, in collaboration with the Holland Computing Center, up to date software and databases in the Life Sciences (specifically bioinformatics) domain.

Provide support for bioinformatics software & analyses on the Holland Computing Cluster. This support is free for up to 3 hours per year per faculty.

The Bioinformatics Core Research Facility receives funding support from the Nebraska Research Initiative (NRI), the Program of Excellence in Computational Sciences, and the NIH via the Nebraska Center for Integrated Biomolecular Communication (NCIBC).

Data deposition of microarray, next-gen, transcriptomes or genomes (per deposition) to public database

$232

$348

$696

Publication-ready graph of any of the above analyses

$66

$99

$198

1) Per analysis (not per sample) additional cost for sparsely annotated species

$200

$280

$560

Custom Bioinformatics Services

Please note that for longer analyses (longer than 10 hours labor) it is more cost-effective for the researcher to pay part of the salary and benefits of the Core's staff. The minimum percentage is 2% fte, approximately a week (5 business days) of a staff's work, and increments by 2%. Note that if payment is made for 2% fte, but staff was able to finish analysis in 3 business days, no refunds are given but the remainder is available to you for further analysis within the same year.

SERVICE DESCRIPTION

UNIV. NEBRASKA

NON-PROFIT/GOVERNMENT

COMMERCIAL

Custom programming/analysis (less than 10 hours)

$90 / h

$140 / h

$275 / h

Custom analysis (more than 10 hours)

Ask for quote

System administration per hosted server or storage cabinet (per year)

$500

N/A

N/A

Instruments & Facilities

The Bioinformatics Core Research Facility houses a high performance Linux compute cluster dedicated to Life Sciences research. In total, the compute cluster has approximately 250 CPU cores, 600GB of RAM, and 400TB of central SAS RAID 6 zfs disk storage.

Most of our cluster nodes have at least 8GB of RAM and are available via the Slurm job scheduling system and are capable of running MPI jobs.

We have a dedicated 4 CPU 6-core large memory server (320 GB RAM) suitable for larger transcriptome and genome assembly jobs. Two web servers and database back-end machines are hosting several UNL database-driven research web sites.

We do not provide access for faculty, staff, or students to our computational cluster anymore, except indirectly via our staff or for the sole purpose of classes or workshops taught by BCRF staff.

In additional to our own cluster, we make heavily use of the University of Nebraska's Holland Computing Center (http://hcc.unl.edu/), on which we also collaborate to keep life sciences software and databases up to date.

Contact the Core Staff

For technical help with bioinformatics software and databases, and analyses using them on the Holland Computing Cluster, we are glad to help out for up to 3 hours gratis per year per faculty. Please use the email listed below to initiate such help; one of us will contact you within a business day. For larger or scientific help, or to initiate discussion on projects, please contact the Director directly instead.